[R] How to use Cox PH model to select genes from DNA gene expression profiles?

[Jerome Asselin]

See the "newdata" argument in ?survfit.

You can use it like this:
cox.surv <- survfit(cox.fit,newdata=selected.genes)
Indeed, you're going to have to build the data frame of your selected genes.

Then see ?plot.survfit for additional plotting options. That'll help you to 
build a "plot(cox.surv,--other arguments--)" command to draw nice survival 
curves.

Hope this helps.

Jerome

On Tuesday 18 February 2003 15:04, Song, Guangchun wrote:
> Content-Length: 355
> Status: R
> X-Status: N
>
>
> I'm doing prediction of the survival cases using gene expression
> profiles(Affymetrix chips).  Can somebody tell me how to use the Cox PH
> model to select genes and make a prediction of survival?
>
>
> Thanks.
>
> Guangchun
>
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-- 

Jerome Asselin (Jérôme)
Statistical Analyst
British Columbia Centre for Excellence in HIV/AIDS
St. Paul's Hospital
608 - 1081 Burrard Street
Vancouver, British Columbia
CANADA V6Z 1Y6

Email: jerome at hivnet.ubc.ca
Phone: 604 806-9112   Fax: 604 806-9044